We used techniques of immunogenetics and molecular biology to study rabbit immunoglobulins, and other genes including RAG-1 and RAG-2, which are necessary for gene rearrangements to occur during lymphocyte development. We investigated the development of anatomical sites such as appendix follicles and germinal centers in gut-associated lymphoid tissues and the regulated expression and sequence diversification of Ig genes during lymphoid cell development. Whereas B cells with rearranged VH1 predominate in normal rabbits, in homozygous Alicia mutant rabbits (ali/ali ) the VH1 gene is deleted and B cells with upstream VH genes rearrange. We found differences between appendix development in normal and ali/ali rabbits based on immunohistochemistry, analyses of cell proliferation and apoptotic death. The development of the appendix in mutants appears to be retarded compared to normals. As populations of B cells bearing VHa2-like epitopes develop in mutant animals, appendix development appears more like normals. A higher proportion of B cells expressing the a2 allotype may receive strong signals to survive rather than undergo apoptosis. VHa2-positive B cells express high levels of Bcl-2 protein compared to a2-negative B cells. This suggests that B cells with FR allotypic motifs may become resistant to programmed cell death via the Bcl-2 pathway. The a2 allotype probably plays functional role(s) in selection and effective expansion of B cells in the appendix. We used the surface markers CD43 and IgM to distinguish two appendix cell populations from 6 to 8-week-old rabbits that expressed RAG-1 transcripts. We speculate that the appearance of CD43 during different stages of B-cell maturation may be related to the function of the appendix as a site of both B-cell development and diversification. IgM associated B cell receptor molecules were found on rabbit B cells as heteromeric structures with nonreduced molecular weights of approximately 75 kDa and 135 kDa composed of 37 and 42 kDa subunits. Immunological studies with monoclonal antibodies suggested that these proteins are the rabbit homologues of murine Ig-beta (B29) and Ig-alpha (mb-1).